ggmcmc: Tools for Analyzing MCMC Simulations from Bayesian Inference

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Tools for assessing and diagnosing convergence of Markov Chain Monte Carlo simulations, as well as for graphically display results from full MCMC analysis. The package also facilitates the graphical interpretation of models by providing flexible functions to plot the results against observed variables.

Author
Xavier Fernández i Marín <xavier.fim@gmail.com>
Date of publication
2016-06-28 23:48:06
Maintainer
Xavier Fernández i Marín <xavier.fim@gmail.com>
License
GPL-2
Version
1.1
URLs

View on CRAN

Man pages

ac
Calculate the autocorrelation of a single chain, for a...
calc_bin
Calculate binwidths by parameter, based on the total number...
ci
Calculate Credible Intervals (wide and narrow).
custom.sort
Auxiliary function that sorts Parameter names taking into...
get_family
Subset a ggs object to get only the parameters with a given...
ggmcmc
Wrapper function that creates a single pdf file with all...
ggs
Import MCMC samples into a ggs object than can be used by all...
ggs_autocorrelation
Plot an autocorrelation matrix
ggs_caterpillar
Caterpillar plot with thick and thin CI
ggs_chain
Auxiliary function that extracts information from a single...
ggs_compare_partial
Density plots comparing the distribution of the whole chain...
ggs_crosscorrelation
Plot the Cross-correlation between-chains
ggs_density
Density plots of the chains
ggs_geweke
Dotplot of the Geweke diagnostic, the standard Z-score
ggs_histogram
Histograms of the paramters.
ggs_pairs
Create a plot matrix of posterior simulations
ggs_ppmean
Posterior predictive plot comparing the outcome mean vs the...
ggs_ppsd
Posterior predictive plot comparing the outcome standard...
ggs_Rhat
Dotplot of Potential Scale Reduction Factor (Rhat)
ggs_rocplot
Receiver-Operator Characteristic (ROC) plot for models with...
ggs_running
Running means of the chains
ggs_separation
Separation plot for models with binary response variables
ggs_traceplot
Traceplot of the chains
gl_unq
Generate a factor with unequal number of repetitions.
radon
Simulations of the parameters of a hierarchical model using...
roc_calc
Calculate the ROC curve for a set of observed outcomes and...
s
Simulations of the parameters of a simple linear regression...
s.binary
Simulations of the parameters of a simple linear regression...
sde0f
Spectral Density Estimate at Zero Frequency.
s.y.rep
Simulations of the posterior predictive distribution of a...
y
Values for the observed outcome of a simple linear regression...
y.binary
Values for the observed outcome of a binary logistic...

Files in this package

ggmcmc
ggmcmc/inst
ggmcmc/inst/CITATION
ggmcmc/inst/doc
ggmcmc/inst/doc/using_ggmcmc.html
ggmcmc/inst/doc/v70i09.pdf
ggmcmc/inst/doc/v70i09.R
ggmcmc/inst/doc/using_ggmcmc.Rmd
ggmcmc/inst/doc/using_ggmcmc.R
ggmcmc/inst/doc/v70i09.Rnw
ggmcmc/NAMESPACE
ggmcmc/NEWS
ggmcmc/data
ggmcmc/data/linear.rda
ggmcmc/data/radon.rda
ggmcmc/data/binary.rda
ggmcmc/R
ggmcmc/R/ggs_histogram.R
ggmcmc/R/ggs.R
ggmcmc/R/ggs_crosscorrelation.R
ggmcmc/R/ggs_separation.R
ggmcmc/R/globals.R
ggmcmc/R/data.R
ggmcmc/R/ggs_Rhat.R
ggmcmc/R/ggs_geweke.R
ggmcmc/R/functions.R
ggmcmc/R/help.R
ggmcmc/R/ggs_autocorrelation.R
ggmcmc/R/ggs_pairs.R
ggmcmc/R/ggs_caterpillar.R
ggmcmc/R/ggs_running.R
ggmcmc/R/ggs_ppsd.R
ggmcmc/R/ggmcmc.R
ggmcmc/R/ggs_compare_partial.R
ggmcmc/R/ggs_traceplot.R
ggmcmc/R/ggs_ppmean.R
ggmcmc/R/ggs_density.R
ggmcmc/R/ggs_rocplot.R
ggmcmc/vignettes
ggmcmc/vignettes/bibliography.bib
ggmcmc/vignettes/v70i09.bib
ggmcmc/vignettes/using_ggmcmc.Rmd
ggmcmc/vignettes/v70i09.Rnw
ggmcmc/README.md
ggmcmc/MD5
ggmcmc/build
ggmcmc/build/vignette.rds
ggmcmc/DESCRIPTION
ggmcmc/man
ggmcmc/man/ci.Rd
ggmcmc/man/ggs_autocorrelation.Rd
ggmcmc/man/ggs_chain.Rd
ggmcmc/man/gl_unq.Rd
ggmcmc/man/ggs_traceplot.Rd
ggmcmc/man/get_family.Rd
ggmcmc/man/ggs_rocplot.Rd
ggmcmc/man/ac.Rd
ggmcmc/man/ggs_ppmean.Rd
ggmcmc/man/ggs.Rd
ggmcmc/man/ggs_compare_partial.Rd
ggmcmc/man/sde0f.Rd
ggmcmc/man/ggs_geweke.Rd
ggmcmc/man/y.Rd
ggmcmc/man/calc_bin.Rd
ggmcmc/man/y.binary.Rd
ggmcmc/man/ggs_Rhat.Rd
ggmcmc/man/custom.sort.Rd
ggmcmc/man/ggs_caterpillar.Rd
ggmcmc/man/ggs_histogram.Rd
ggmcmc/man/ggs_ppsd.Rd
ggmcmc/man/s.binary.Rd
ggmcmc/man/radon.Rd
ggmcmc/man/s.y.rep.Rd
ggmcmc/man/roc_calc.Rd
ggmcmc/man/ggs_pairs.Rd
ggmcmc/man/ggs_crosscorrelation.Rd
ggmcmc/man/s.Rd
ggmcmc/man/ggmcmc.Rd
ggmcmc/man/ggs_separation.Rd
ggmcmc/man/ggs_density.Rd
ggmcmc/man/ggs_running.Rd